GROMACS version:
GROMACS modification: Yes/No
Hello dear friends,
I am performing Gmx_mmpbsa on a lipid embedded nanotube system which is a drug delivery system for transferring a drug. I have done Steered molecular dynamics on this system and now I need to calculate the binding energy of the drug and the nanotube rings as it passes through the tube. However, I have faced an error which says that the atom number of the drug does not exist and match the index file and it is not in range. I have checked the .tpr, topology and index file, they are correct and also the ones which I used for md simulation. The only thing that comes to my mind is that since I have added the atom coordinates of the drug manually to the .pdb and then .gro input file system of smd simulation (after performing docking calculations), the name of the molecule in the index and topology files is different from the .gro file. I tried to change the name but it did not work and now I don’t know what to do since probably the .xtc file is the problem?
If you have faced this before or if you have any suggestions regarding this issue, I will appreciate your help.
Thank you in advance.